http://www.mdpi.com/journal/microarrays Latest open access articles published in Microarrays at http://www.mdpi.com/journal/microarrays http://www.mdpi.com/2076-3905/2/2/115 Microarray technology allows monitoring of gene expression profiling at the genome level. This is useful in order to search for genes involved in a disease. The performances of the methods used to select interesting genes are most often judged after other analyzes (qPCR validation, search in databases...), which are also subject to error. A good evaluation of gene selection methods is possible with data whose characteristics are known, that is to say, synthetic data. We propose a model to simulate microarray data with similar characteristics to the data commonly produced by current platforms. The parameters used in this model are described to allow the user to generate data with varying characteristics. In order to show the flexibility of the proposed model, a commented example is given and illustrated. An R package is available for immediate use. Microarrays 2013-04-17 2 2 Article 10.3390/microarrays2020115 115 130 2076-3905 2013-04-17 doi: 10.3390/microarrays2020115 Doulaye Dembélé http://www.mdpi.com/2076-3905/2/2/97 Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This requires functional manipulation of these genes and networks in laboratory models of normal and diseased cells. One approach is to assess molecular and biological responses to high-throughput RNA interference (RNAi)-induced gene knockdown. These responses can be revealed by immunofluorescent staining for a molecular or cellular process of interest and quantified using fluorescence image analysis. These applications are typically performed in multiwell format, but are limited by high reagent costs and long plate processing times. These limitations can be mitigated by analyzing cells grown in cell spot microarray (CSMA) format. CSMAs are produced by growing cells on small (~200 mm diameter) spots with each spot carrying an siRNA with transfection reagent. The spacing between spots is only a few hundred micrometers, thus thousands of cell spots can be arranged on a single cell culture surface. These high-density cell cultures can be immunofluorescently stained with minimal reagent consumption and analyzed quickly using automated fluorescence microscopy platforms. This review covers basic aspects of imaging-based CSMA technology, describes a wide range of immunofluorescence assays that have already been implemented successfully for CSMA screening and suggests future directions for advanced RNAi screening experiments. Microarrays 2013-04-11 2 2 Article 10.3390/microarrays2020097 97 114 2076-3905 2013-04-11 doi: 10.3390/microarrays2020097 Juha Rantala Sunjong Kwon James Korkola Joe Gray http://www.mdpi.com/2076-3905/2/2/81 Cardiovascular development is a complex process in which several transcriptional pathways are operative, providing instructions to the developing cardiomyocytes, while coping with contraction and morphogenetic movements to shape the mature heart. The discovery of microRNAs has added a new layer of complexity to the molecular mechanisms governing the formation of the heart. Discrete genetic ablation of the microRNAs processing enzymes, such as Dicer and Drosha, has highlighted the functional roles of microRNAs during heart development. Importantly, selective deletion of a single microRNA, miR-1-2, results in an embryonic lethal phenotype in which both morphogenetic, as well as impaired conduction, phenotypes can be observed. In an effort to grasp the variability of microRNA expression during cardiac morphogenesis, we recently reported the dynamic expression profile during ventricular development, highlighting the importance of miR-27 on the regulation of a key cardiac transcription factor, Mef2c. In this review, we compare the microRNA expression profile in distinct models of cardiogenesis, such as ventricular chamber development, induced pluripotent stem cell (iPS)-derived cardiomyocytes and the aging heart. Importantly, out of 486 microRNAs assessed in the developing heart, 11% (55) displayed increased expression, many of which are also differentially expressed in distinct cardiogenetic experimental models, including iPS-derived cardiomyocytes. A review on the functional analyses of these differentially expressed microRNAs will be provided in the context of cardiac development, highlighting the resolution and power of microarrays analyses on the quest to decipher the most relevant microRNAs in the developing, aging and diseased heart. Microarrays 2013-04-03 2 2 Review 10.3390/microarrays2020081 81 96 2076-3905 2013-04-03 doi: 10.3390/microarrays2020081 Fernando Bonet Francisco Hernandez-Torres Franciso Esteban Amelia Aranega Diego Franco http://www.mdpi.com/2076-3905/2/2/63 Microarray technology has become a very popular approach in cases where multiple experiments need to be conducted repeatedly or done with a variety of samples. In our lab, we are applying our high density spots microarray approach to microscopy visualization of the effects of transiently introduced siRNA or cDNA on cellular morphology or phenotype. In this publication, we are discussing the possibility of using this micro-scale high throughput process to study the role of microRNAs in the biology of selected cellular models. After reverse-transfection of microRNAs and siRNA, the cellular phenotype generated by microRNAs regulated NF-κB expression comparably to the siRNA. The ability to print microRNA molecules for reverse transfection into cells is opening up the wide horizon for the phenotypic high content screening of microRNA libraries using cellular disease models. Microarrays 2013-04-03 2 2 Article 10.3390/microarrays2020063 63 80 2076-3905 2013-04-03 doi: 10.3390/microarrays2020063 Yong-Jun Kwon Jin Heo Hi Kim Jin Kim Michel Liuzzi Veronica Soloveva http://www.mdpi.com/2076-3905/2/2/51 The role of gene deletion and duplication in the aetiology of disease has become increasingly evident over the last decade. In addition to the classical deletion/duplication disorders diagnosed using molecular techniques, such as Duchenne Muscular Dystrophy and Charcot-Marie-Tooth Neuropathy Type 1A, the significance of partial or whole gene deletions in the pathogenesis of a large number single-gene disorders is becoming more apparent. A variety of dosage analysis methods are available to the diagnostic laboratory but the widespread application of many of these techniques is limited by the expense of the kits/reagents and restrictive targeting to a particular gene or portion of a gene. These limitations are particularly important in the context of a small diagnostic laboratory with modest sample throughput. We have developed a gene-targeted, custom-designed comparative genomic hybridisation (CGH) array that allows twelve clinical samples to be interrogated simultaneously for exonic deletions/duplications within any gene (or panel of genes) on the array. We report here on the use of the array in the analysis of a series of clinical samples processed by our laboratory over a twelve-month period. The array has proven itself to be robust, flexible and highly suited to the diagnostic environment. Microarrays 2013-03-27 2 2 Article 10.3390/microarrays2020051 51 62 2076-3905 2013-03-27 doi: 10.3390/microarrays2020051 Renate Marquis-Nicholson Debra Prosser Jennifer Love Donald Love http://www.mdpi.com/2076-3905/2/2/34 Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels) to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1) the total number of target genes is large enough (>10,000); and (2) the expression level of the majority of genes is kept constant. However, microRNA (miRNA) arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays. Microarrays 2013-03-25 2 2 Review 10.3390/microarrays2020034 34 50 2076-3905 2013-03-25 doi: 10.3390/microarrays2020034 Bin Wang Yaguang Xi http://www.mdpi.com/2076-3905/2/1/24 Mature microRNA is a crucial component in the gene expression regulation network. At the same time, microRNA gene expression and procession is regulated in a precise and collaborated way. Pre-microRNAs mediate products during the microRNA transcription process, they can provide hints of microRNA gene expression regulation or can serve as alternative biomarkers. To date, little effort has been devoted to pre-microRNA expression profiling. In this study, three human and three mouse microRNA profile data sets, based on the Affymetrix miRNA 2.0 array, have been re-analyzed for both mature and pre-microRNA signals as a primary test of parallel mature/pre-microRNA expression profiling on a single platform. The results not only demonstrated a glimpse of pre-microRNA expression in human and mouse, but also the relationship of microRNA expressions between pre- and mature forms. The study also showed a possible application of currently available microRNA microarrays in profiling pre-microRNA expression in a time and cost effective manner. Microarrays 2013-03-14 2 1 Communication 10.3390/microarrays2010024 24 33 2076-3905 2013-03-14 doi: 10.3390/microarrays2010024 Lin Gan Bernd Denecke http://www.mdpi.com/2076-3905/2/1/1 Harmful algal blooms (HABs) occur worldwide, causing health problems and economic damages to fisheries and tourism. Monitoring agencies are therefore essential, yet monitoring is based only on time-consuming light microscopy, a level at which a correct identification can be limited by insufficient morphological characters. The project MIDTAL (Microarray Detection of Toxic Algae)—an FP7-funded EU project—used rRNA genes (SSU and LSU) as a target on microarrays to identify toxic species. Furthermore, toxins were detected with a newly developed multiplex optical Surface Plasmon Resonance biosensor (Multi SPR) and compared with an enzyme-linked immunosorbent assay (ELISA). In this study, we demonstrate the latest generation of MIDTAL microarrays (version 3) and show the correlation between cell counts, detected toxin and microarray signals from field samples taken in Arcachon Bay in France in 2011. The MIDTAL microarray always detected more potentially toxic species than those detected by microscopic counts. The toxin detection was even more sensitive than both methods. Because of the universal nature of both toxin and species microarrays, they can be used to detect invasive species. Nevertheless, the MIDTAL microarray is not completely universal: first, because not all toxic species are on the chip, and second, because invasive species, such as Ostreopsis, already influence European coasts. Microarrays 2013-03-05 2 1 Article 10.3390/microarrays2010001 1 23 2076-3905 2013-03-05 doi: 10.3390/microarrays2010001 Jessica Kegel Yolanda Del Amo Laurence Costes Linda Medlin http://www.mdpi.com/2076-3905/1/3/107 This overview describes microarray-based tests that combine solution-phase amplification chemistry and microarray hybridization within a single microfluidic chamber. The integrated biochemical approach improves microarray workflow for diagnostic applications by reducing the number of steps and minimizing the potential for sample or amplicon cross-contamination. Examples described herein illustrate a basic, integrated approach for DNA and RNA genomes, and a simple consumable architecture for incorporating wash steps while retaining an entirely closed system. It is anticipated that integrated microarray biochemistry will provide an opportunity to significantly reduce the complexity and cost of microarray consumables, equipment, and workflow, which in turn will enable a broader spectrum of users to exploit the intrinsic multiplexing power of microarrays for infectious disease diagnostics. Microarrays 2012-11-09 1 3 Review 10.3390/microarrays1030107 107 124 2076-3905 2012-11-09 doi: 10.3390/microarrays1030107 Darrell Chandler Lexi Bryant Sara Griesemer Rui Gu Christopher Knickerbocker Alexander Kukhtin Jennifer Parker Cynthia Zimmerman Kirsten George Christopher Cooney http://www.mdpi.com/2076-3905/1/2/95 A sandwich microarray employing two distinct aptamers for human thrombin has been optimized for the detection of subnanomolar concentrations of the protein. The aptamer microarray demonstrates high specificity for thrombin, proving that a two-site binding assay with the TBA1 aptamer as capture layer and the TBA2 aptamer as detection layer can ensure great specificity at times and conditions compatible with standard routine analysis of biological samples. Aptamer microarray sensitivity was evaluated directly by fluorescent analysis employing Cy5-labeled TBA2 and indirectly by the use of TBA2-biotin followed by detection with fluorescent streptavidin. Sub-nanomolar LODs were reached in all cases and in the presence of serum, demonstrating that the optimized aptamer microarray can identify thrombin by a low-cost, sensitive and specific method. Microarrays 2012-08-08 1 2 Article 10.3390/microarrays1020095 95 106 2076-3905 2012-08-08 doi: 10.3390/microarrays1020095 Anna Meneghello Alice Sosic Agnese Antognoli Erica Cretaio Barbara Gatto http://www.mdpi.com/2076-3905/1/2/84 Quality control and normalization is considered the most important step in the analysis of microarray data. At present there are various methods available for quality assessments of microarray datasets. However there seems to be no standard visualization routine, which also depicts individual microarray quality. Here we present a convenient method for visualizing the results of standard quality control tests using Circos plots. In these plots various quality measurements are drawn in a circular fashion, thus allowing for visualization of the quality and all outliers of each distinct array within a microarray dataset. The proposed method is intended for use with the Affymetrix Human Genome platform (i.e., GPL 96, GPL570 and GPL571). Circos quality measurement plots are a convenient way for the initial quality estimate of Affymetrix datasets that are stored in publicly available databases. Microarrays 2012-08-07 1 2 Article 10.3390/microarrays1020084 84 94 2076-3905 2012-08-07 doi: 10.3390/microarrays1020084 Martin Koch Michael Wiese http://www.mdpi.com/2076-3905/1/2/64 Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation. Microarrays 2012-08-06 1 2 Review 10.3390/microarrays1020064 64 83 2076-3905 2012-08-06 doi: 10.3390/microarrays1020064 Paula Díez Noelia Dasilva María González-González Sergio Matarraz Juan Casado-Vela Alberto Orfao Manuel Fuentes http://www.mdpi.com/2076-3905/1/1/44 Withania somnifera (L.) Dunal (Indian ginseng, winter cherry, Solanaceae) is widely used in traditional medicine. Roots are either chewed or used to prepare beverages (aqueous decocts). The major secondary metabolites of Withania somnifera are the withanolides, which are C-28-steroidal lactone triterpenoids. Withania somnifera extracts exert chemopreventive and anticancer activities in vitro and in vivo. The aims of the present in silico study were, firstly, to investigate whether tumor cells develop cross-resistance between standard anticancer drugs and withanolides and, secondly, to elucidate the molecular determinants of sensitivity and resistance of tumor cells towards withanolides. Using IC50 concentrations of eight different withanolides (withaferin A, withaferin A diacetate, 3-azerininylwithaferin A, withafastuosin D diacetate, 4-B-hydroxy-withanolide E, isowithanololide E, withafastuosin E, and withaperuvin) and 19 established anticancer drugs, we analyzed the cross-resistance profile of 60 tumor cell lines. The cell lines revealed cross-resistance between the eight withanolides. Consistent cross-resistance between withanolides and nitrosoureas (carmustin, lomustin, and semimustin) was also observed. Then, we performed transcriptomic microarray-based COMPARE and hierarchical cluster analyses of mRNA expression to identify mRNA expression profiles predicting sensitivity or resistance towards withanolides. Genes from diverse functional groups were significantly associated with response of tumor cells to withaferin A diacetate, e.g. genes functioning in DNA damage and repair, stress response, cell growth regulation, extracellular matrix components, cell adhesion and cell migration, constituents of the ribosome, cytoskeletal organization and regulation, signal transduction, transcription factors, and others. Microarrays 2012-05-22 1 1 Article 10.3390/microarrays1010044 44 63 2076-3905 2012-05-22 doi: 10.3390/microarrays1010044 Thomas Efferth Henry Johannes Greten http://www.mdpi.com/2076-3905/1/1/42 Microarrays covers research where microarrays are applied to address complex biological questions. This new open access journal publishes articles where novel applications or state-of-the art technology developments in the field are reported. In addition, novel methods or data analysis algorithms are under the scope of Microarrays. This journal will serve as a platform for fast and efficient sharing of data within this large user community. As one of the first microarray users in Europe back in 1996, I am proud to serve as Editor-in-Chief and I believe we have assembled a highly proficient Editorial Board, responsible for a fair and fast peer-review of articles. Microarrays 2011-11-22 1 1 Editorial 10.3390/microarrays1010042 42 43 2076-3905 2011-11-22 doi: 10.3390/microarrays1010042 Ulrich Certa http://www.mdpi.com/2076-3905/1/1/25 A functional biodiversity microarray (EcoChip) prototype has been developed to facilitate the analysis of fungal communities in environmental samples with broad functional and phylogenetic coverage and to enable the incorporation of nucleic acid sequence data as they become available from large-scale (next generation) sequencing projects. A dual probe set (DPS) was designed to detect a) functional enzyme transcripts at conserved protein sites and b) phylogenetic barcoding transcripts at ITS regions present in precursor rRNA. Deviating from the concept of GeoChip-type microarrays, the presented EcoChip microarray phylogenetic information was obtained using a dedicated set of barcoding microarray probes, whereas functional gene expression was analyzed by conserved domain-specific probes. By unlinking these two target groups, the shortage of broad sequence information of functional enzyme-coding genes in environmental communities became less important. The novel EcoChip microarray could be successfully applied to identify specific degradation activities in environmental samples at considerably high phylogenetic resolution. Reproducible and unbiased microarray signals could be obtained with chemically labeled total RNA preparations, thus avoiding the use of enzymatic labeling steps. ITS precursor rRNA was detected for the first time in a microarray experiment, which confirms the applicability of the EcoChip concept to selectively quantify the transcriptionally active part of fungal communities at high phylogenetic resolution. In addition, the chosen microarray platform facilitates the conducting of experiments with high sample throughput in almost any molecular biology laboratory. Microarrays 2011-10-31 1 1 Article 10.3390/microarrays1010025 25 41 2076-3905 2011-10-31 doi: 10.3390/microarrays1010025 Derek Peršoh Alfons R. Weig Gerhard Rambold http://www.mdpi.com/2076-3905/1/1/3 Reliable and sensitive pathogen detection in clinical and environmental (including food and water) samples is of greatest importance for public health. Standard microbiological methods have several limitations and improved alternatives are needed. Most important requirements for reliable analysis include: (i) specificity; (ii) sensitivity; (iii) multiplexing potential; (iv) robustness; (v) speed; (vi) automation potential; and (vii) low cost. Microarray technology can, through its very nature, fulfill many of these requirements directly and the remaining challenges have been tackled. In this review, we attempt to compare performance characteristics of the microbial diagnostic microarrays developed for the detection and typing of food and water pathogens, and discuss limitations, points still to be addressed and issues specific for the analysis of food, water and environmental samples. Microarrays 2011-10-14 1 1 Review 10.3390/microarrays1010003 3 24 2076-3905 2011-10-14 doi: 10.3390/microarrays1010003 Tanja Kostić Angela Sessitsch http://www.mdpi.com/2076-3905/1/1/1 Our publishing company MDPI AG has its headquarters in Basel, Switzerland where there are thousands of scientists working in the laboratories of pharmaceutical companies and institutes including Novartis [1], F. Hoffmann-La Roche [2] and institutes affiliated with University of Basel [3]. In 1996, the first annual microplate conference MipTec was held in Basel, and the MipTec 2011 was held a few days ago in Basel [4]. I published a paper on microplate standardization presented at MipTec 1996 in MDPI’s longest-running journal Molecules [5-7]. [....] Microarrays 2011-10-14 1 1 Editorial 10.3390/microarrays1010001 1 2 2076-3905 2011-10-14 doi: 10.3390/microarrays1010001 Shu-Kun Lin